I currently have two female rescue Guinea Pigs, Pita and Panini. We got Panini as a companion for Pita, housed them separately for some time, then in adjacent cages, then divided the current cage and have now opened the entire 12.5 square feet to the both of them. They have two of everything, and there are no hides with single openings.
During the entire process, Panini was fairly aggressive towards Pita but we figured it was just a dominance issue. We cleaned the entire cage and bathed both of them, but Panini is still being aggressive towards Pita.
It’s to the point where Pita doesn’t move from one corner all day and night. She won’t even let Pita use any of the hides. Panini will relentlessly bite her until she’s back in the corner.
What should I do? I love Panini but Pita is the priority and clearly is not happy.

She was listed as senior but they didn’t give an exact age, I don’t think the previous owners knew. She has not been checked for ovarian cysts to my knowledge, but I can contact the rescue and ask. I know she was pregnant when she was dropped off at the rescue, I don’t know if pregnancy has any impact on the likeliness of cysts.

Only other thing I can think of is draping multiple pieces of fringed fleece to run through and visually block view of the other guinea pig. You do indeed want to weigh frequently to ensure she is not losing weight. As PooksiedAnimals notes, that really is "the last straw".

Ditto bpatters. Read www.guinealynx.info/ovarian_cysts.html for more info. A guinea pig with ovarian cysts can have hormonal imbalances that affect behavior and result in a more aggressive female.

I agree, and tell the vet to look for very small ones too. My vet said that the most aggressive sows have tiny ones. Bubbly was like that. Despite that, Kooky never had any ovarian cysts, and she became much nicer to the others when we put her in a cage double the required size. She loved other pigs, but needed her space more than others I ever had.

I expanded the cage quite a bit; it went from 3x3 (grids) to 3x5! So now it’s 1.9 square meters which is nearly twice the recommended size. Hopefully that’ll help. I’m also going to make a vet appointment for both of them in case it’s a medical issue. Thank you all for your help!

It sounds like the cage is plenty big enough. If they still don't get along, go back to putting a partition between them and let them live side by side. There's nothing wrong with letting them do that. They can still see and hear each other through the grids and get the benefit of companionship.

Having them checked out at the vet is a wonderful idea and will give you peace of mind if nothing is wrong. Has Panini ever shown any signs of mites? That can make a pig pretty uncomfortable and possibly aggressive toward other pigs. Then again, it might just be her personality.